Metroid Shinji
by Toby860
Summary: What would happen if almost imediatly after being abandoned by his father Shinji were to be thrust into galactic war and was raised by an ancient alien race along with the galaxies best bounty hunter.


**Disclaimer: I own nothing but my original characters.**

For my story Basic is English and I will elaborate later in the story

Chapter 1

A little boy of six sits at a train station crying his eyes out as his father rides away. The last thing the father said to the boy was "I have no use for you anymore."

The boy just sits there waiting for a man his father has told him is coming to pick him up. Suddenly he hears a noise that sounds like fighting. Right in front of the station the boy sees these weird lizard-like bipedal monsters shooting orange orbs at other tall bird-like monsters that were returning fire.

Unknown to the boy one of the lizard like monsters had gotten shot and in its confusion looked up at the boy and thought it was one of the chozo that had confronted the pirates when they were going to raid the planet. The pirate aimed at the boy, tightened its grip, and fired. The shot hit the boy on the right side of his chest where the lung is located. One of the chozo sees this and fires a super missile at the pirate group killing the remaining pirates.

The leader of the chozo assault party, Noct'earl, walks up to where the boy lays in blood gasping for breath. The bird-like beast said something in a language that was foreign to the boy and sounded like scratchy whistles and grunts. [_Mor'Lac get over here we have a wounded humanoid who caught by a shot from a pirates nova beam._]

[_I'm here Noct'earl, how bad does it look in your eyes? You are more familiar with humanoids than anybody else in the group.]_

_[It's bad Mor'Lac, from what I can tell the shot completely destroyed his right lung, as well as burning and puncturing several other organs including; the liver, kidney, and pancreas, and if that were not enough a peace of one of his ribs has lodged in his heart and will kill him if he does not get treatment back on the Rukongai.]_

_[So what do you recommend my old friend?]_

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While this was going on the boy regained consciousness and immediately noticed the two standing over him talking in that scratchy speech. Then he glanced around and noticed other activity. The rest of the birdmen were piling the bodies of the dead in a pile and looked like they were going to lite it on fire. He then looked back to the 'men' above him and tried to speak but could only groan but it was enough to get their attention.

_[Hurry up Mor'Lac he is going into something called shock where his body shuts down because of what has happened and it will kill him faster than the wound if we don't treat him back on the RUKONGAI.]_

_[Then what Noct'earl, what happens after we bring him aboard and treat him. Do we just send him back down here where he would be left alone and when he is found is surrounded by all this destruction he is taken away and examined by the government. Do we keep him and raise him what about his family.]_

_[Don't worry Mor'Lac, when he awakens we will ask him what he wants to do. For now we will bring him aboard and treat him with the same nanite treatment I gave Samus. DOES ANYBODY HAVE ANY OBJECTIONS? If he decides to stay we can implement all the same changes I initiated in samus, but one thing that must be done is the uploading of Basic that way we can communicate with him.]_

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(As this was going on they had lifted the boy onto a hoverstretcher and were heading back to the shuttle to take them to the Rukongai)

'_What is going on?' _the boy thought '_The last thing I remember was my father leaving and then there was these weird creatures and it looked like they were fighting. Then there was this pain in the right side of my chest and it became hard to breath.'_

(At this point the pain became too much for the boy to handle and he passed out.)

(At this time the party had arrived at the shuttle and returned to the main ship and were prepping the Rukongai to leave earth's orbit)

The chozo are prepping the Rukongai for launch as Mor'Lac is in the medical area and is working on changing the machines to Noct'earl's specifications as to make it able to heal shinji. He was working as the shuttle launched and engaged its cloaking device as to be undetected by any earth radar. Noct'earl comes in and stands over in the shadows like a guardian angel as Mor'Lac hooked up all the leads and needles to shinji and walked over to the console that would activate the Bio-Electron Allocation Module and start healing shinji. Curious to Mor'Lac was how the BEAM looked like a chrome plated MRI machine used in earth hospitals.

_[It's ready Noct'earl. All I have to do is press the code sequence and the machine will activate, spreading nanites in shinji's body and having them work on repairing the damage done by that nova beam blast.]_

_[Good. Thank you Mor'Lac for preparing the BEAM as fast as you did. Start the process and save his life.]_

_[You got it Noct'earl activating.]_

The machine starts making noise and shining a pulsating blue and green light. The readout on the monitor saying that shinji would be unconscious for an hour but after that it would wake him up per instructions. Noct'earl and Mor'Lac leave the med bay and head up to the bridge. With Noct'earl calling his pseudo daughter to report to the bridge as he wants to talk to her.

(Time skip 1 hour)

As shinji slowly opens his he notices a few things. One he is in a medical room and is hooked up to a machine that is slowly beeping and has a 3d holographic display of his body that is being examined. The second thing is that two of the bird-like beings are in the room with him and are looking over the 3D display. The third is that he isn't alone in his bed and that there is a little girl who also looks six lying on her side with her left arm thrown across his chest and her head nuzzling his neck.

"WH-Where am I." He asks to no-one in particular but he gets a response none the less.

"You're in the medical bay." The little girl answers.

"Who are you?" He asks her as he is confused as to her answering his question shows knowledge of this place that he has a inkling of a feeling that is not of human design, or for that matter, might not even be from earth.

"I'm sorry I haven't introduced myself or my father. My name is Samus. Samus Aran but my friends call me Sammy. So you will be calling me Sammy right?" She responds and then asks shinji while giving him her version of a puppy dog face and in the process breaks his heart because he thinks she looks really cute when she does that with her shoulder length blond hair and sea blue eyes.

"Uh yea ok. Soooo Sammy who is your father?"

"Oh I forgot about him. See the one in the red armor that is my papa. His name is Noct'earl but I just call him papa. He is the one that brought you onboard."

"Oh ok. What is he?"

"He is an alien called a Chozo."

_[Ah look Noct'earl the boy is awake and from what I can hear from your daughters conversation with him his name is shinji]_

_[It looks like he is getting along with samus alright. She will be able to keep him calm while we talk with him.]_

_[Not we Noct'earl. I need to go see how the preparations to leave orbit are going. When you are done talking with him give me a message and we will leave based on his decision]_

_[Fine you traitor I will see you on the bridge in a little while.]_

_[With your permission captain] _Mor'Lac says and salutes before he leaves.

Noct'earl walks over to the boy's bed and sits in a chair. He then makes himself comfortable while gathering his thoughts on how he is going to talk to the boy and ask him questions. He was unlucky as the boy asked him a question.

"Mister Noct'earl what happened? How did I get here? The last place I was at was the train station."

"_I must say for your first time speaking basic you are doing well and as for how you got here I brought you after you were injured by a shot from a space pirate nova beam."_

"What exactly is a space pirate?"

"_A space pirate is a reptilian space creature that is a criminal and murder. They kill others and steal their stuff. Except this is whole specie and they are doing this on a planet wide scale. We currently are at war with them and at the station we had confronted an assault squad and engaged them. One of the dying pirates saw you and mistook you for one of us and shot you in the chest with a nova beam. To save your life we had to bring you onboard and operate using nanites and genetic mapping. Now I must ask Why were You there all alone?"_

Shinji sniffs before he responds and as his eyes tear up he says "My mom is dead. She died yesterday and my dad brought me there before he left me saying he had no use for me anymore. I was waiting for a man to come and pick me up that I'm supposed to live with."

"_I see and how old are you Shinji?"_

"I'm six"

"_Well shinji I have an idea. Why don't you come with us? I know a fellow chozo who would want to take you in and raise you. Plus samus can use a playmate. Why not come with us back to our planet and live with us. We will keep an eye out incase if you are needed for anything but you basically leave earth behind. What do you think? Do you want to come?"_

Shinji thinks it over and he doesn't see any reason to stay so slowly he nods and immediately gets tackled and is given a full body hug by samus.

She says "This is so awesome. Now I have somebody to hang out with now and play and train. Hey dad can we bring him to the bridge so we can see the ship leave earth behind?"

"_Sure would you like to see it shinji?"_

"Yes I would sir thank you for taking me with you."

"_Don't worry about it when we get to Tallon IV you will meet your guardian."_

The three of them walk to a turbo lift and ride it up to the bridge where Mor'Lac is barking orders in chozo to the bridge techs.

_We're ready to leave Mor'Lac on your mark engage the Trans-Light Drive."_

"_You got it sir. Alright ladies lets go. Engage. So you decided to stay shinji?"_

The viewing screen in front of them turns white for a second before showing space with stars flying past.

"Yes sir I did and what do I call you?"

"_Just call me MorL and if you are unsure of what to call Noct'earl take a leaf from my kids book and call him uncle Knuckle. He may act mad but in truth he doesn't mind."_

"I will thanks sir oops I mean MorL." He then walks over to where samus is standing and stands next to her. She sees him there and grabs his hand and gently squeezes it to give him comfort.

"Don't worry I will always be your friend and I have met your guardian. She is a good person."

"Thanks Sammy" He smiles at the girl and she smiles back.

(10 Years Later)

'I hope Sammy put the ship in a safe place' the boy named Sylux thinks. He had renamed himself but back here on earth he has to go by his birth name of Shinji Ikari. He placed the phone back in its receiver after hearing it repeat the message three times "we are sorry but Tokyo-3 is in a state of emergency and all civilians are to report to emergency shelters. Thank you for your Co-operation."

"Is everything alright Sye?" The blond haired blue eyed 16 year old named Samus Aran asked her partner Brown haired grey eyed Sylux formerly known as shinji ikari.

"I'm not sure Sammy but let's see what happens."

EVIL EARLY CLIFFHANGER

Authors Notes:

Well here is the first chapter of my first story. I will be using flashbacks and dreams and I will even write several chapters throughout this whole story that will give you an idea of what shinji's/Sylux's life was like growing up. I got this Idea after playing every Metroid game in story timeline order. For those wondering Italics are when a chozo are speaking."" Mean speaking, '' are thoughts, [] are being spoken in chozo. The capitalized letter in a chozo name following the ' like in Mor'Lac means he is married or the chozo equivalent of a life partner. As such Samus's father Noct'earl is alone. I am unsure if I will continue this story so please review and give me your thoughts on how I did. Also I am having a contest to think up of a name for shinji's chozo guardian/pseudo mother so whoever gives me the best idea will be used and mentioned in the next chapter. She is going to be single so go from there. For those of you who are wondering what the Rukongai looks like I am borrowing the look of a sovereign class battleship from Star Trek. Ultimately this will be a shinji/samus pairing. They are already boyfriend and girlfriend but have not taken the final step and lost their virginity. I will rate this M as their will be lemon is some of the followings. Also shinji is not going to be a pushover but will have balls and be brave or he will totally be OOC. Thank you for reading my Notes on the subject. Read and Review.

Alexis Svitkona


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